Assembly of 454 raw data (in fastq)

Question

[bird77]

I need to assemble raw reads from a project that already has been published. The metagenome was sequenced with 454, but the files are only present in fastq format.

Is there an assembler which is up-to-date which can assemble long 454 reads with this quality profile? Can UDBA or Megahit deal with that?

Or does anyone have different recommendations?

Thank you for your help.

[Joe]

I thought (though I may well be wrong) that Velvet or SOAP was originally developed for 454 sequencing.

Answer 1

[colindaven]

Newbler always worked pretty well with 454. Otherwise CLC genomics was also easy.

Can Spades deal with it for a more modern option ?

[Joe]

I don't think so. I use SPAdes fairly frequently and never noticed any information suggesting it does, but I am guessing a bit.